You say "Separating the documentation could be safer". I've found that keeping the documentation in the same file as the code make it more likely that it will be updated when the code changes; you don't have to find the doc file. Personally, I'd say that it's safer to have up-to-date docs.

My initial response to this matter is that, all things considered, perhaps you should just examine all of the scripts and write a Word document that contains whatever comments you wish to make about them. Simply talk to “the equally befuddled persons who are doomed to come after you,” and help them along. I don’t necessarily interpret this requirement to mean that you should add POD-comments to each file. (But, if at-all in doubt,ask your manager who gave you this assignment!!)

My opinion of Doxygen is that (a) it unquestionably delivers to you “what its designers intended,” but (b) that it is not terribly useful. It is, after all, merely a digital algorithm. I suspect that you have been tasked to “dive in to all of this (mess) and (please) come up with a useful set of bread-crumbs.” If Doxygen can provide you with a useful-to-you and-to-your successors part,</em. then by all means use it. But you, as a human being, will have to go from there to produce a final-product that is useful to the team.

Ada Lovelace for the palindrome
Albert Einstein for having smelly feet
Alfred Nobel for his contribution to battlefield science
Burkhard Heim for providing the missing link between science and mysticism
Claude Shannnon for riding a unicycle at night at MIT
Donald Knuth for being such a great organist
Edward Teller for being the template for Dr. Strangelove
Edwin Hubble for pretending to be a pipe-smoking English gentleman
Erwin Schrödinger for cruelty to cats
Hedy Lamarr for weaponizing pianos
Hugh Everett for immortality, especially for cats
Isaac Newton for his occult studies
Kikunae Ikeda for discovering the secrets of soy sauce
Larry Wall for his website
Louis Camille Maillard for discovering why steaks taste good
Marie Curie for the shiny stuff
Nikola Tesla for the cool cars
Paul Dirac for speaking one word per hour when socializing
Richard Feynman for his bongo skills
Robert Oppenheimer for his in-depth knowledge of the Bhagavad Gita
Rusi P Taleyarkhan for Cold Fusion
Sigmund Freud for his Ménage ā trois
Theodor W Adorno for his contribution to the reception of jazz
Wilhelm Röntgen for the foundations of body scanners
Yulii Borisovich Khariton for the Tsar Bomba
Other (please explain why)